Multimeric Protein Purity Determination

ABSTRACT

Improved capillary zone electrophoresis (CZE), affinity capillary electrophoresis (ACE), and partially filled-ACE (PF-ACE) systems and methods for the detection and quantification of specific molecular entities in a mixture thereof are provided. During manufacturing, heterodimeric bispecific antibodies are often produced along with homodimer species, which can confound quantification of the bispecific antibody. Disclosed are capillary electrophoretic systems and methods of detecting a specific homodimer in the mixture of bispecific heterodimer and homodimers. A ligand capable of binding one of the subunits of the bispecific antibody is contacted with the mixture to form a complex having a reduced electrophoretic mobility, thereby enabling detection of the unbound homodimer.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. application Ser. No.15/152,135, filed on May 11, 2016, which claims the benefit of priorityunder 35 USC § 119(e) of U.S. Provisional Patent Application No.62/160,341, filed May 12, 2015, which application is herein specificallyincorporated by reference in its entirety.

SEQUENCE LISTING

A WIPO Standard ST.25 (1998) compliant text file of a sequence listingis filed concurrently with the present specification. The contents ofthe text file are herein incorporated by reference. The text filecontaining the sequence listing is named “10141US01_ST25” was created onApr. 11, 2016, and contains about 19,025 bytes of information.

BACKGROUND Field

The invention is generally directed to compositions, systems and methodsfor detecting one or more species of polypeptide in a complex mixture ofpolypeptides and polypeptide complexes. Specifically, the inventionincludes compositions, systems and methods for detecting homodimers in amixture of multimers that include bispecific antibodies.

Related Art

Monoclonal antibodies represent an important class of therapeutics forvarious diseases. There is a growing interest in increasing theversatility of monoclonal antibodies, with one approach being the designand generation of bispecific antibodies (bsAb). Conventional expressionof a bsAb using two heavy and two light chains will result in multiple(up to ten) undesirable multimeric protein products due to the randomassociation of heavy and light chains. Co-expression of two unique heavychains and one common light chain will minimize the number of sideproducts to two homodimeric species, which may need to be subsequentlyremoved during purification. Thus, a need for effective and efficientmethods to detect and differentiate homodimer side products from thedesired heterodimer (bsAb) exists. Reagents and methods to estimate thepurity of a bsAb consisting of two unique heavy chains and two identicallight chains are disclosed.

SUMMARY

Applicants have developed reagents and processes to detect homodimerside products within a mixture of multimeric products. The reagentsinclude a ligand that binds to a specific subunit of the homodimer sideproducts. The processes include modified forms of capillary zoneelectrophoresis (CZE) called affinity capillary electrophoresis (ACE),in which the ligand is combined with the mixture of multimeric productsprior to electrophoresis; and partially filled affinity capillaryelectrophoresis (PF-ACE), in which the capillary is partially filledwith the ligand prior to electrophoresing the mixture of multimericproducts. The multimeric products include a heterodimer, which containsa first subunit and a second subunit; a first homodimer, which containstwo first subunits (a.k.a. “homo-B”); and a second homodimer, whichcontains two second subunits (a.k.a. “homo-A”). The ligand binds to aspecific subunit, in some embodiments to the first subunit, and in otherembodiments, the second subunit.

In one embodiment, the mixture of multimeric proteins is produced bycells containing heterologous nucleic acids that express the firstsubunit and the second subunit. In particular embodiments, the cells aremammalian cells used in the industrial scale production ofbiotherapeutic molecules like monoclonal antibodies. Cells include CHOcells and their derivatives—CHO-K1 cells and EESYR® cells.

In one embodiment, the homodimer (either the first homodimer or thesecond homodimer) is detected via capillary zone electrophoresis bydecreasing the charge/mass ratio of the heterodimer and other homodimer.The charge/mass is decreased when one of the ligands binds to one of thesubunits, resulting in the formation of a complex having a decreasedcharge/mass, which greatly slows the mobility of the complex through thecapillary relative to the unbound subunit and its homodimer. Forexample, when the multimer mixture is combined with the ligand thatbinds to the second subunit (second ligand), that second ligand willbind to the heterodimer (which contains a first subunit and a secondsubunit) and the second homodimer (which contains two second subunits).The first homodimer remains unbound and therefore has a higher charge tosize ratio and concomitant increased mobility through the capillary.Thus, during electrophoresis, the first homodimer peak is detected firstand its peak is well separated from the complexed second homodimer andheterodimers. Likewise, when the multimer mixture is combined with thefirst ligand, the electrophoretic mobility of the complexed firsthomodimer and the heterodimer is decreased, allowing the secondhomodimer to be detected as a well separated peak. This procedure iscalled affinity capillary electrophoresis (ACE).

In another embodiment, the capillary is pre-loaded with the ligand plug.When the mixture of multimers is loaded and electrophoresed through thecapillary, each multimer species will encounter the “ligand plug” in thecapillary. Any multimer containing a subunit that binds to the ligandwill bind the ligand and its electrophoretic mobility will be retarded(i.e., mobility shift). The unbound homodimer is then free to movethrough the capillary separated from the ligand-bound multimers. Thisprocedure is called partially filled-affinity capillary electrophoresis(PF-ACE).

To detect both the first homodimer and the second homodimer, at leasttwo separate procedures are performed, one using the first ligand todetect the second homodimer, and one using the second ligand to detectthe first homodimer. Optionally, a standard CZE procedure may be run todetect the heterodimer, which having a similar charge/mass to bothhomodimers will be detected in the same “peak” as the homodimers. Theheterodimer fraction is quantified by subtracting the first homodimerdetected in the first ACE or PF-ACE procedure, and subtracting thesecond homodimer likewise detected in the second procedure.

In one embodiment, the first subunit contains an immunoglobulin CH3domain that enables the first subunit to bind protein A, and the secondsubunit contains a variant immunoglobulin CH3 domain that does notenable the second subunit to bind protein A. In one embodiment, eachhomodimer is a monospecific antibody having a distinct specificity, andthe heterodimer is a bispecific antibody specific for both the cognateantigen of the first homodimer and the cognate antigen of the secondhomodimer. In one embodiment, each of the three antibodies (e.g., bsAbor hetero-AB, homo-A, homo-B) contains identical light chains, and thefirst and second subunits refer to heavy chains. While the antibodiesare referred to as homodimers and heterodimers, they are usuallyactually tetramers. Since the light chains are the same for eachmultimeric species, they are essentially ignored for the purposes ofnomenclature. In a specific embodiment, the first heavy chain can bindto protein A, and the second heavy chain contains the H95R and Y96Fsubstitutions of the CH3 domain, which abrogates protein A binding(numbering according to IMGT; see Lefranc, M.-P., (2008) 40 Mol.Biotechnol. 101-111).

In one embodiment, the ligand is an antibody that binds to a subunit.The first ligand is an antibody that binds to the first subunit, but notto the second subunit; and the second ligand is an antibody that bindsto the second subunit, but not to the first subunit. In one embodiment,the pI (isoelectric point) of the ligand is different or modified to bedifferent than the pI of each of the multimers (e.g., more acidic orlower pI).

DRAWINGS

FIG. 1 is a schematic diagram depicting a bispecific antibody(hetero-AB) and the product-related side-products (homo-A and homo-B)expressed during production. The dipeptide substitution in the CH3domain lacking protein A binding is indicated by the filled six-pointedstar.

FIG. 2 depicts electropherograms of homo-A (a), homo-B (b), bsAb1 (c),mixture of homo-A, homo-B, and bsAb (d) and a molecular weight ladder(e) analyzed by CE-SDS under reducing conditions.

FIG. 3 depicts representative electropherograms of bsAb1 (trace a),homo-B mAb (trace b), homo-A mAb (trace c) and a 1:2:1 mixture ofhomo-A:bsAb1:homo-B (traced) separated via CZE.

FIG. 4 depicts CZE electropherograms of bsAb2 (trace a), homo-B (traceb), and homo-A (trace c) mAbs.

FIG. 5 depicts electropherograms of bsAb3 (trace A) samples, bsAb3 inthe presence of anti-A mAb (trace B), and bsAb3 in the presence ofanti-B mAb (trace C) affinity ligand.

FIG. 6 depicts a SE-HPLC chromatogram depicting the stoichiometricbinding of the chain-B specific ligand to the bsAb3. Trace a depictsbsAb3, trace b depicts anti-B antibody, and trace c depicts thecombination of bsAb3 and anti-B antibody.

FIG. 7 depicts electropherograms of bsAb-3 (trace A) samples, in thepresence of anti-chain B ligand under ACE (trace B) and PF-ACE (trace C)conditions.

FIG. 8 depicts electropherograms of free homo-B mAb (trace A), homo-BmAb in the presence of either anti-chain-B mAb (trace B) or anti-chain-AmAb (trace C). Electropherograms of free homo-A mAb (trace D) and homo-AmAb in the presence of either anti-chain-A mAb (trace E) or anti-chain-BmAb (trace F) are also shown.

FIG. 9 depicts electropherograms of bsAb3 (trace a), and bsAb3 spikedwith 5% of mAb impurities (trace b) in the presence of either anti-A mAb(trace c) or anti-B mAb (trace d).

FIG. 10 depicts the corrected peak area for homodimer A (homo-A) overrelative concentration (percent) of homo-A.

FIG. 11 depicts the corrected peak area for homodimer B (homo-B) overrelative concentration (percent) of homo-B.

DETAILED DESCRIPTION

Before the present invention is described, it is to be understood thatthis invention is not limited to particular methods and experimentalconditions described, as such methods and conditions may vary. It isalso to be understood that the terminology used herein is for thepurpose of describing particular embodiments only, and is not intendedto be limiting, since the scope of the present invention will be limitedonly by the appended claims.

Although any methods and materials similar or equivalent to thosedescribed herein can be used in the practice or testing of the presentinvention, the preferred methods and materials are now described. Allpublications cited herein are incorporated herein by reference todescribe in their entirety. Unless defined otherwise, all technical andscientific terms used herein have the same meaning as commonlyunderstood by one of ordinary skill in the art to which this inventionbelongs.

As used herein, the term “ligand” means any molecule that binds toanother molecule. “Ligand” has the traditional meaning in thebiochemical arts as an agonist or antagonist that binds to a cognatereceptor. “Ligand” as used herein also encompasses the antibody-antigeninteraction, in which the antibody is the ligand and the antigen is itscognate binding partner, or vice versa in which the antigen is theligand and the antibody (or fragment thereof) is the cognate bindingpartner.

A ligand may be any molecule that binds to a “cognate” molecule,including antibodies, antibody fragments, ScFv molecules, trapmolecules, receptor concatamers, recombinant or synthetic moleculescontaining one or more CDRs, antigens, haptens, recombinant epitopes,canonical ligans, receptors, soluble receptor fragments, nuclearreceptors, steroids, peptides, aptmers, RNAs, DNAs, organic molecules,small molecules, and the like.

The term “ligand plug” refers to a ligand-rich area within thecapillary, generally near the loading end (e.g., near the anode end) ofthe capillary. The capillary can be pre-loaded with ligand, which formsa “plug” that binds to (i.e., “captures”) the ligand's cognate bindingpartner as that cognate binding partner migrates along the capillary,forming a “complex” that has an altered mobility.

The term “complex” refers to and includes higher order molecularentities comprising at least two molecular entities, such as smallmolecules, metals, polypeptides, proteins, nucleic acids, aptamersorother molecular entities. The term “complex” includes multisubunitproteins. For example, hemoglobin is a complex containing two alphaglobin chains, two beta globin chains, four iron-containing heme groups,and CO₂ or O₂. For example, a receptor bound to its cognate ligand is acomplex, an antibody bound to an antigen is a complex, and an enzymebound to a substrate or bound to a substrate and a cofactor is acomplex. As used in some embodiments herein disclosed, “complex”includes a homodimer or heterodimer bound to a ligand. A complex mayalso be referred to as “molecular entity” or “entity”. For example, ahomodimer or heterodimer bound to its ligand, which is a complex, mayitself be referred to as an “entity” or “molecular entity”

As used herein, the term “multimer” and the phrase “multimeric protein”are used interchangeably to denote a protein made of more than onecomponent subunit. The subunits may be bound together or otherwiseassociated to form the multimer. The binding or association may be viaany one or more intermolecular bonds, including covalent andnon-covalent bonds. A “homodimer” is a multimer comprising two or moresubunits that are the same or functionally equivalent. As used herein, ahomodimer comprises at least two polypeptide chains that are the same orfunctionally equivalent, but the homodimer may include additionalsubunits as well. For example, a monoclonal antibody contains twoidentical heavy chains. As such, the monoclonal antibody may beconsidered to be a “homodimer”. However, a complete canonical monoclonalantibody also contains two light chains and thus can be referred to as atetramer. A “heterodimer” is a multimer comprising two or more subunitsthat are not the same or are not functionally equivalent. Theheterodimer may contain additional subunits beside the two dissimilarsubunits. For example, a bispecific antibody contains two heavy chainsand two light chains, such that one half of the antibody (e.g., oneheavy chain and one light chain) binds one epitope and the other half ofthe antibody (e.g., another heavy chain and the same light chain, thesame heavy chain and another light chain, or another light chain andanother heavy chain) specifically binds to another epitope. Thebispecific antibody is a tetramer. In some cases, the bispecific is aheterodimer as that term relates to the heavy chains not being the sameor not being functionally equivalent.

As used herein, the term “subunit” or “component subunit” or means acomponent of a multimer, usually (but not always) a polypeptide. Thecomponent polypeptide is a single chain and can be of any size fromthree amino acids to several thousands of amino acids long.

As used herein, the term “bind” or the term “bound” means theassociation one molecule with another through non-covalent forces. Tobind or to be bound implies a relatively strong force (micromolar orbelow Kd), such as that between an antibody and its antigen, or a ligandand its receptor. Non-covalent forces include hydrogen bonding,ion-dipole and ion-induced dipole interactions, ionic interaction, Vander Waals forces, hydrophobic interaction, halogen bonding, pi-piinteractions, and cation pi-anion pi interaction. See Wang et al.,(2001) 30 Ann. Rev. Biophys. Biomol Structure 211-243.

The term “attach”, “crosslink”, “attached”, or “crosslinked” isgenerally used to convey the covalent association of two or moresubunits to form a more complex protein.

The terms “CH3”, “CH3 domain”, and “immunoglobulin CH3 domain” are usedinterchangeably and denote the region of an immunoglobulin heavy chainspanning from about amino acid 341 to the C-terminus according to the EUnumbering system (Edelman et al., (1969) 63(1) Proc. Natl. Acad. Sci.USA. 78-85). The CH3 domain is involved in protein A binding, such thatfor example the CH3 domains of human IgG1, IgG2, and IgG4 modulateprotein A binding, but the CH3 domain of IgG3 does not (Van Loghem etal., Staphylococcal protein A and human IgG subclasses and allotypes,15(3) Scand. J. Immunol. 275-8 (1982)). Amino acid substitutions H95Rand Y96F in the CH3 domain (IMGT numbering; H435R and Y436F in the EUnumbering system) abrogates protein A binding (U.S. Pat. No. 8,586,713(issued Nov. 19, 2013)).

As used herein, the term “antibody” refers to an immunoglobulin moleculeconsisting of four polypeptide chains, two heavy (H) chains and twolight (L) chains inter-connected by disulfide bonds. Each heavy chainhas a heavy chain variable region (HCVR or VH) and a heavy chainconstant region. The heavy chain constant region contains three domains,CH1, CH2 and CH3. Each light chain has a light chain variable region anda light chain constant region. The light chain constant region consistsof one domain (CL). The VH and VL regions can be further subdivided intoregions of hypervariability, termed complementarity determining regions(CDR), interspersed with regions that are more conserved, termedframework regions (FR). Each VH and VL is composed of three CDRs andfour FRs, arranged from amino-terminus to carboxy-terminus in thefollowing order: FR1, CDR1, FR2, CDR2, FR3, CDR3, FR4. The term“antibody” includes reference to both glycosylated and non-glycosylatedimmunoglobulins of any isotype or subclass. The term “antibody” includesantibody molecules prepared, expressed, created or isolated byrecombinant means, such as antibodies isolated from a host celltransfected to express the antibody. For a review on antibody structure,see Lefranc et al., IMGT unique numbering for immunoglobulin and T cellreceptor variable domains and Ig superfamily V-like domains, 27(1) Dev.Comp. Immunol. 55-77 (2003); and M. Potter, Structural correlates ofimmunoglobulindiversity, 2(1) Surv. Immunol. Res. 27-42 (1983).

The term antibody also encompasses “bispecific antibody”, which includesa heterotetrameric immunoglobulin that can bind to more than onedifferent epitope. One half of the bispecific antibody, which includes asingle heavy chain and a single light chain and six CDRs, binds to oneantigen or epitope, and the other half of the antibody binds to adifferent antigen or epitope. In some cases, the bispecific antibody canbind the same antigen, but at different epitopes or non-overlappingepitopes. In some cases, both halves of the bispecific antibody haveidentical light chains while retaining dual specificity. Bispecificantibodies are described generally in U.S. Patent App. Pub. No.2010/0331527(Dec. 30, 2010).

The term “antigen-binding portion” of an antibody (or “antibodyfragment”), refers to one or more fragments of an antibody that retainthe ability to specifically bind to an antigen. Examples of bindingfragments encompassed within the term “antigen-binding portion” of anantibody include (i) a Fab fragment, a monovalent fragment consisting ofthe VL, VH, CL and CH1 domains; (ii) a F(ab′)2 fragment, a bivalentfragment comprising two Fab fragments linked by a disulfide bridge atthe hinge region; (iii) a Fd fragment consisting of the VH and CH1domains; (iv) a Fv fragment consisting of the VL and VH domains of asingle arm of an antibody, (v) a dAb fragment (Ward et al. (1989) Nature241:544-546), which consists of a VH domain, (vi) an isolated CDR, and(vii) an scFv, which consists of the two domains of the Fv fragment, VLand VH, joined by a synthetic linker to form a single protein chain inwhich the VL and VH regions pair to form monovalent molecules. Otherforms of single chain antibodies, such as diabodies are also encompassedunder the term “antibody” (see e.g., Holliger et al. (1993) 90 PNAS USA6444-6448; and Poljak et al. (1994) 2 Structure 1121-1123).

Still further, an antibody or antigen-binding portion thereof may bepart of a larger immunoadhesion molecule, formed by covalent ornoncovalent association of the antibody or antibody portion with one ormore other proteins or peptides. Examples of such immunoadhesionmolecules include use of the streptavidin core region to make atetrameric scFv molecule (Kipriyanov et al. (1995) 6 Human Antibodiesand Hybridomas 93-101) and use of a cysteine residue, a marker peptideand a C-terminal polyhistidine tag to make bivalent and biotinylatedscFv molecules (Kipriyanov et al. (1994) 31 Mol. Immunol. 1047-1058).Antibody portions, such as Fab and F(ab′)2 fragments, can be preparedfrom whole antibodies using conventional techniques, such as papain orpepsin digestion of whole antibodies. Moreover, antibodies, antibodyportions and immunoadhesion molecules can be obtained using standardrecombinant DNA techniques commonly known in the art (see Sambrook etal., 1989).

“Fc fusion proteins” comprise part or all of two or more proteins, oneof which is an Fc portion of an immunoglobulin molecule, which are nototherwise found together in nature. Preparation of fusion proteinscomprising certain heterologous polypeptides fused to various portionsof antibody-derived polypeptides (including the Fc domain) has beendescribed, e.g., by Ashkenazi et al., (1991) 88 Proc. Natl. Acad. Sci.USA 10535; Byrn et al., (1990) 344 Nature 677; and Hollenbaugh et al.,(1992) “Construction of Immunoglobulin Fusion Proteins”, in CurrentProtocols in Immunology, Suppl. 4, pages 10.19.1-10.19.11. “Receptor Fcfusion proteins” comprise one or more extracellular domain(s) of areceptor coupled to an Fc moiety, which in some embodiments comprises ahinge region followed by a CH2 and CH3 domain of an immunoglobulin. Insome embodiments, the Fc-fusion protein contains two or more distinctreceptor chains that bind to one or more ligand(s). For example,Fc-fusion protein is a trap, such as for example an IL-1 trap (e.g.,rilonacept, which contains the IL-1RAcP ligand binding region fused tothe IL-1R1 extracellular region fused to Fc of hIgG1; see U.S. Pat. No.6,927,004), or a VEGF trap (e.g., aflibercept, which contains the Igdomain 2 of the VEGF receptor Flt1 fused to the Ig domain 3 of the VEGFreceptor Flk1 fused to Fc of hIgG1; see U.S. Pat. No. 7,087,411 (issuedAug. 8, 2006) and 7,279,159 (issued Oct. 9, 2007)).

The term “protein A” as used herein means natural forms, recombinantforms, modified forms, engineered forms and derivatives of the 42 kDaStapylococcus aureus cell wall protein A that bind to the Fc domains ofIgG1, IgG2 and IgG4, but not to IgG3 (Dima et al., (1983) 13(8) Eur. J.Immunol. 605-14). Engineered protein A may be for example a Z-domaintetramer, a Y-domain tetramer, or an engineered protein A that lacks Dand E domains. These engineered protein A exemplars are unable to bind(or bind with very low affinity if at all) to the VH3 domain of animmunoglobulin, but can still bind to the CH3 domains of IgG1, IgG2 andIgG4. Engineered protein A is discussed in Minakuchi et al., (2013)22(9) Protein Sci. 1230-8. Commercially available proteins include MabSelect® (GE Healthcare, Little Chalfont, UK), Mab Select Sure (GEHealthcare, Piscataway, N.J.) Prosep Ultra® (Millipore, Billerica,Mass.), and Poros A® (Perspective Biosystems, Framingham, Mass.).

Protein A affinity chromatography makes use of the affinity of protein Afor the Fc domain to purify Fc-containing proteins. In practice, proteinA chromatography involves using protein A immobilized to a solidsupport. See Gagnon, Protein A Affinity Chromotography, PurificationTools for Monoclonal Antibodies, Validated Biosystems 155-198 (1996).The solid support is a non-aqueous matrix onto which protein A adheres.Such supports include agarose, sepharose, glass, silica, polystyrene,nitrocellulose, charcoal, sand, cellulose and any other suitablematerial. Methods for affixing proteins to suitable solid supports arewell known in the art. See e.g. Ostrove, (1990) in Guide to ProteinPurification, Methods in Enzymology, 182: 357-371. Such solid supports,with and without immobilized protein A, are readily available from manycommercial sources such as Vector Laboratory (Burlingame, Calif.), SantaCruz Biotechnology (Santa Cruz, Calif.), BioRad (Hercules, Calif.),Amersham Biosciences (part of GE Healthcare, Uppsala, Sweden), Pall(Port Washington, N.Y.) and EMD-Millipore (Billerica, Mass.). Protein Aimmobilized to a pore glass matrix is commercially available asPROSEP®-A (Millipore). The solid phase may also be an agarose-basedmatrix. Protein A immobilized on an agarose matrix is commerciallyavailable as MABSELECT™ (GE Healthcare Bio-Sciences, Pittsburgh, Pa.).

The term “capillary” refers to a substrate through or upon which one ormore molecular entities travel, in some cases at different rates toallow for separation. A capillary can be made of any material, such asglass or a polymer. For example, bare fused silica capillaries (40 or 50μm) were used in some experiments exemplified below (available fromPolymicro Technologies, Phoenix, Ariz.). A capillary can be a hollowtube of a length that is greater than its diameter. A capillary isgenerally used to separate biomolecules or other molecular entitiesbased upon the mass and/or charge of the entity. For example, when anelectric potential is placed across the capillary, the molecularentities migrate through the capillary at a rate determined by theircharge to size ratio. To provide the electrical potential, one end ofthe capillary is linked to a cathode (negative charge) (“cathode end ofthe capillary”) and the other end of the capillary is linked to an anode(positive charge) (“anode end of the capillary”). Positive-chargedentities will migrate toward the cathode.

A “detector” or “detector window” is provided at a point along the longaxis of the capillary, to serve as a window to detect molecular entitiesas they pass by. Molecular entities can be detected by any one or moreof methods known in the molecule detection arts. For example, proteinscan be detected by absorbance of electromagnetic radiation at 220 nm or280 nm (DNA at 260 nm) (“UV absorbance detection”). See C. Stoscheck,(1990) 182 Methods in Enzymology 50-69. Laser-induced fluorescence(CE-LIF) may also be employed to detect molecular entities by nativefluorescence (for those molecules having native fluorescence) ordetection of labeled entities. For example, a 280 nm or 295 nm laser canbe used to induce the natural fluorescence of tyrosine, tryptophan andphenylalanine of proteins, and the emitted light is detected (e.g., theBeckman Coulter PA 800 Protein Characterization System, Beckman Coulter,Brea, Calif.). Molecular entities may also be detected by LIF byderivatizing the entity with fluorophore tags, exciting the derivatizedentity with a laser (e.g., argon-ion laser emitting at 488 nm, HeCdlaser emitting at 442 nm, or diode laser emitting at 473, 410, 405, or425 nm), and detecting the emission wavelength. Those tags include interalia fluorescein isothiocyanate (FITC), carboxyfluorescein succinimidylester (CFSE), 6-oxy-(N-succininmidyl acetate)-9-(2-methoxycarbonyl)(SAMF), N-hydroxysuccinimidyl fluorescein-O-acetate (SIFA),4-fluoro-7-nitro-2,1,3-benzoxadiazole (NBD-F),3-(2-furoyl)quinoline-2-carboxaldehyde (FQ),5-(4,6-dichrolotriazinyl)aminofluorescein (DTAF) and3-(4-carboxybenzoyl)-2-quinolinecarbox-aldehyde (CBQCA). See E. Szökö &T. Tábi, (2010) 53(5) J. Pharma. and Biomed. Analysis 1180-1192.

The term “cell” refers to a prokaryotic or a eukaryotic cell. A cell iscapable of expressing a polypeptide or protein that is useful inter aliaas a reagent or as a therapeutic drug (Kipriyanov and Little, (1999) 12Molecular Biotechnology 173-201). The expressed polypeptide or proteinmay localize within the cell, localize at the cell membrane or cellwall, or be secreted from the cell. Prokaryotic cells include bacterialcells like Escherichia coli (Spaduit et al., (2014) 32(1) TrendsBiotechnol. 54-60). Eukaryotic cells include plant cells like tobacco,Arabidopsis, potato, maize, carrot, and safflower (Yusibov et al.,(2011) 7:3 Human Vaccines 313-321; K. Ko, (2014) 33(3) MonoclonalAntibodies in Immunodiagnosis and Immunotherapy 192-198). Eukaryoticcells include yeast cells like Saccaromyces cerevisiae and Pichiapastoris (Spaduit, et al., (2011) 3(5) MAbs 453-60). Eukaryotic cellsinclude insect cells like 519 cells (Huang et al., (2006) 26(2A)Anticancer Res. 1057-63). Eukaryotic cells include mammalian cells likeBSC cells, HeLa cells, HepG2 cells, LLC-MK cells, CV-1 cells, COS cells,VERO cells, MDBK cells, MDCK cells, CRFK cells, RAF cells, RK cells,TCMK-1 cells, LLCPK cells, PK15 cells, LLC-RK cells, MDOK cells, BHKcells, BHK-21 cells, “CHO cells”, CHO-K1 cells, EESYR® cells, NS-1cells, MRC-5 cells, WI-38 cells, BHK cells, 3T3 cells, 293 cells, RKcells, Per.C6 cells and chicken embryo cells. A “Chinese hamster ovary(CHO) cell line” or one or more of several specific CHO cell variants,such as the CHO-K1 cell line are optimized for large-scale proteinproduction, such as in the production of antibodies. The EESYR® cellline is a specialized CHO cell line optimized for enhance production ofproteins of interest. For a detailed description of EESYR® cells, seeU.S. Pat. No. 7,771,997 (issued Aug. 10, 2010).

The term “mobility” refers to the movement of a molecular entity(including a complex) through a medium. The medium can be a gel, a film,air or other gas, aqueous buffer or other liquid, a capillary, a thinfilm, sieving particles, or the like. The molecular entity may movethrough inter alia an electric field, a magnetic field, a gravitationalfield, by simple diffusion, or via molecular sieving. Mobility isgenerally related to the volume, mass, or charge of the molecularentity. For diffusion, a molecular entity having a larger mass has lowermobility than an entity or complex having a smaller mass. Mobility of amolecular entity in an electric field (i.e., “electrophoretic mobility”)depends on the charge-to-mass ratio of the entity. The charge of theentity depends in part upon the three dimensional structure of theentity, its isoelectric point, its state of denaturation or nativity,its state of solvation and hydration, the buffer and pH of the medium.See Barroso et al., (2015) 854 Analytica Chimica Acta 169-177. Thegreater the charge to size ratio of the molecular entity, the greaterthe electrophoretic mobility (i.e., higher velocity through the medium).

Ligands

In one aspect, the invention provides a ligand that binds a firstsubunit of a multisubunit protein and does not bind a second subunit ofthe multisubunit protein. The ligand is used to identify those moleculesthat contain a first subunit, either directly or indirectly throughsubtraction. In an alternate embodiment, the ligand binds to the secondsubunit, and not the first subunit. Generally, the ligand binds to onesubunit of a heterodimer, but not to the other subunit of theheterodimer.

In some cases, each of the first and second subunits contains animmunoglobulin CH3 domain. Since an immunoglobulin heavy chain containsa CH3 domain, each subunit may be an immunoglobulin heavy chain. Themultisubunit protein therefore in some cases is an antibody containingtwo distinct heavy chains. Such an antibody can be a bispecific antibodyhaving dual epitope specificity.

According to some protocols for producing bispecific antibodies (orother heteromultimers), the CH3 domain of one subunit is capable ofbinding to protein A (CH3), and the CH3 of the other subunit does notbind protein A or binds it at a much reduced affinity (CH3*). Thebispecific antibody therefore binds protein A better than an antibodywith two CH3 domains that having reduced or no protein A binding ability(i.e., CH3*), but not as well as the antibody with two protein A-bindingCH3 domains. This differential binding to protein A can be used toseparate the bispecific antibody from any homodimers that are present.In one embodiment, the CH3* comprises amino acid substitutions H95R andY96F (numbered according to the IMGT exon numbering system), whichreduce or abrogate protein A binding.

For example, a bispecific antibody can be produced by expressing in acell (e.g., CHO cell or CHO cell-derivative such as EESYR®) both a firstheavy chain specific to a first epitope, and a second heavy chainspecific to a second epitope. Since the antibody contains two heavychains, at least three forms of antibody would be produced by the cell:a homodimer specific to the first epitope having two identical firstheavy chains (a.k.a. homo-B), a homodimer specific to the second epitopehaving two identical second heavy chains (a.k.a. homo-A), and aheterodimer specific to both epitopes and having both a first and asecond heavy chain (a.k.a. hetero-AB). In some purification schema, theseparation of the protein A-binding homodimer (homo-B) and the proteinA-binding heterodimer (hetero-AB) is less than perfect and the resultantheterodimer (e.g., bispecific antibody) is contaminated with homodimer.

One particular object of the invention is to determine the purity ofheterodimer produced by cells and purified by protein A chromatographyby distinguishing the homodimers from the heterodimer. In some cases,the biophysical attributes of the homodimers and the heterodimer (Ab)(e.g., mass, isoelectric point, amino acid content, and the like) aresimilar enough to make specific identification and quantification ofeach species difficult. The ligand (L) is therefore used to selectivelybind one of the homodimers and the heterodimer, and not bind the otherhomodimer. Such binding forms a complex (a.k.a. Ab·L) that has alteredand distinguishing biophysical attributes, which enables the skilledartisan to distinguish the non-bound homodimer from the bound homodimerand bound heterodimer. In some cases the complex has alteredelectrophoretic mobility, which allows for greater separation orresolution of the uncomplexed homodimer from the ligand-associatedcomplexes.

The ligand may be an antibody, antibody fragment, or otherantigen-binding protein that specifically binds to one of the subunits(e.g., either the first subunit or the second subunit, but not both). Inone embodiment, wherein (a) the heterodimer is a bispecific antibody,(b) the first subunit is an immunoglobulin heavy chain containing theCH3 domain that binds protein A, (c) the second subunit is animmunoglobulin heavy chain containing the CH3 domain that does not bindprotein A (e.g., the CH3* containing the H95R and Y96F amino acidsubstitutions), and (d) the ligand is an antibody that binds the firstsubunit, the ligand comprises heavy chain complementarity determiningregions (HCDR) 1, 2 and 3 comprising the amino acid sequences set forthin SEQ ID NO:1, SEQ ID NO:2, and SEQ ID NO:3, respectively, and/or lightchain complementarity determining regions (LCDR) 1, 2 and 3 comprisingthe amino acid sequences set forth in SEQ ID NO:4, SEQ ID NO:5, and SEQID NO:6, respectively (e.g., anti-B antibody).

In another embodiment, wherein (a) the heterodimer is a bispecificantibody, (b) the first subunit is an immunoglobulin heavy chaincontaining the CH3 domain that binds protein A, (c) the second subunitis an immunoglobulin heavy chain containing the CH3 domain that does notbind protein A (e.g., the CH3* containing the H95R and Y96F amino acidsubstitutions), and (d) the ligand is an antibody that binds the secondsubunit, the ligand comprises heavy chain complementarity determiningregions (HCDR) 1, 2 and 3 comprising the amino acid sequences set forthin SEQ ID NO:7, SEQ ID NO:8, and SEQ ID NO:9, respectively, and/or lightchain complementarity determining regions (LCDR) 1, 2 and 3 comprisingthe amino acid sequences set forth in SEQ ID NO:10, SEQ ID NO:11, andSEQ ID NO:12, respectively (e.g., anti-B antibody).

System for Detecting or Quantifying Bispecific Antibodies

Bispecific antibodies (bsAbs) possess two distinct bindingspecificities, and have a wide range of clinical applications, includingcancer therapy (Kufer et al., (2004) 22(5) Trends Biotechnol. 238-44;and Lameris et al., (2014) S1040-8428 (14) Crit. Rev. Oncol. Hematol.2014, 00135-8.) BsAbs can cross-link and activate heterodimericreceptors, which are otherwise challenging to activate via traditionalcombination drug therapy or monotherapy (J. R. Cochran, (2010) 2(17) SciTransl Med. 17ps5).

The manufacture of bsAbs at commercial scale is challenging. Multipleapproaches have been adopted to generate viable bsAbs suitable fortherapeutic use (R. E. Kontermann (2012) 4:2 MAbs 182-97). One suchapproach involves the use of a common light chain covalently linking twounique heavy chains (chain-A and chain-B) (Davis et al., PCT App. No.WO2010151792, Dec. 29, 2010; 2011; Babb et al., PCT App. No.WO2013184761, Dec. 12, 2013). The first heavy chain (a.k.a. “firstsubunit”, or “chain-B”), the second heavy chain (a.k.a. “secondsubunit”, or “chain-A”) and the common light chain are co-expressedduring production and are then assembled into three products: homo-A,homo-B and hetero-AB. Homodimers (homo-A or homo-B), consist of twoidentical heavy chains (AA or BB) and two identical light chains. ThebsAb product (hetero-AB) consists of two unique heavy chains (chain-Aand chain-B) and two identical light chains. Theoretically, the threeproducts should be expressed in a ratio or 1:2:1 (homo-A, hetero-AB andhomo-B) (FIG. 1). One of the heavy chains, chain-A, abrogates binding toprotein A and it allows selective purification of the bsAb (hetero-AB),resulting from intermediate binding affinity to protein A column whencompared to the tighter binding of homo-B, or the weaker binding ofhomo-A monospecific Abs.

Despite all these advances in the manufacturing of bsAbs, small amountsof homodimers (homo-A and homo-B) could still be present in purifiedbsAb drugs. Depending on its target antigen, even a small amount ofhomodimer could potentially exhibit a different mode of action ordifferent degradation pathway and hence impact potency andimmunogenicity of the bsAb product (Woods et al., (2013) 5 mAbs711-722). Therefore, it is critical to develop an analytical method toassess the purity of bsAbs.

The structural and physiochemical similarities between the homodimericproduct impurities and heterodimer make separation and quantificationextremely difficult. Traditional separation-based purity assays such asgel electrophoresis and size-exclusion chromatography lack theresolution to distinguish bsAbs from their homodimeric impurities.Recently, an LC-MS based approach to estimate the purity of bsAb hasbeen reported (Id.). Although mass spectrometry is routinely applied incharacterizing the purity of bsAbs, its application to quantify bsAbsover homodimers involves modifications such as deglycosylation.Heterogeneity arising from ionization velocity and truncation ofC-terminal lysine further limits the application of mass spectrometryfor the purity assessment of bsAbs.

Capillary Electrophoresis (CE) is used to characterize antibodies(Jorgenson et al., (2000) 72 Anal. Chem. 111-128). Forms of CE includecapillary electrophoresis-sodium dodecyl sulfate (CE-SDS), capillaryiso-electric focusing (cIEF) and capillary zone electrophoresis (CZE).The separation mechanism of CZE is based on charge to size ratio. CZE isemployed in some antibody assays using uncoated capillaries (He et al.,(2010) 82(8) Anal. Chem. 3222-30). Also, CZE combined withpartially-filled affinity capillary electrophoresis (PF-ACE) has beenused to determine the identity of particular molecular species (Brown etal., (2005) 540 Analytica Chimica Acta 403-410). PF-ACE takes advantageof the shift in mobility of the analyte (e.g., bsAb, homo-A and homo-B)due to its selective affinity towards chain specific ligands. PF-ACE canbe employed orthogonal to the existing LC-MS based approach (Woods,2013).

In another aspect, the invention provides a system, e.g. a CZE system,comprising a ligand, a first homodimer, a second homodimer, aheterodimer, a capillary, a detector, an anode at or near one end of thecapillary, a cathode at or near the other end of the capillary, and apower supply. In one embodiment, the first homodimer comprises at leasttwo identical first subunits (e.g., immunoglobulin heavy chains capableof binding to protein A), the second homodimer comprises at least twoidentical second subunits (e.g., immunoglobulin heavy chains incapableof binding to protein A), and the heterodimer comprises one firstsubunit and one second subunit. The detector can be positioned anywherealong the capillary. Generally, the molecular entities will have anoverall positive charge and therefore migrate toward the cathode underan electric field. Therefore, in some embodiments, the detector ispositioned near the cathode end of the capillary. The detector candetect protein and may employ inter alia a UV detection method, in whichlight absorbance at 210 nm or 280 nm is measured, or laser inducedfluorescence, in which native fluorescence or fluorescent labels aredetected.

In one embodiment, the ligand (which is specific for either the firstsubunit or the second subunit, but not both), the first homodimer, thesecond homodimer, and the heterodimer are loaded onto the capillary ator near the anode end of the capillary. In some cases, the mixture canbe loaded near the cathode end or at any position along the capillary.The ligand binds to its cognate subunit and forms a complex with theheterodimer and one of the homodimers, but not the other homodimer.Thus, when the ligand binds to the first subunit, complexes comprisingthe first homodimer and the ligand (first complex), and the heterodimerand the ligand (second complex) are formed. Alternatively, when theligand binds to the second subunit, complexes comprising the secondhomodimer and the ligand (third complex), and the heterodimer and theligand (fourth complex) are formed. In each case, the complexes have alower electrophoretic mobility than the unbound (uncomplexed) homodimer.In some embodiments, i.e., when the heterodimer is a bispecificantibody, the first subunit is an immunoglobulin heavy chain that iscapable of binding protein A, and the second subunit is animmunoglobulin heavy chain that is incapable of binding protein A (i.e.,containing the H95R and Y96F substituted CH3* domain.)

According to this system and method, the complexes are retarded duringprogression through the capillary and do not cross the detector windowat the same time as the uncomplexed homodimer. The uncomplexed homodimeris therefore detected and quantified free of any interfering heterodimerand other homodimer. In the case of bispecific antibodies, one ACE assayuses the ligand that binds to the unsubstituted CH3 heavy chain, inwhich the CH3*:CH3* (homo-A) dimer remains uncomplexed. The CH3*:CH3*(homo-A) homodimer is detected and quantified. The other independent ACEassay (which may be run separately and/or in parallel to the first ACEassay) uses the ligand that binds to the H95R and Y96F substituted CH3*domain. Here, the CH3:CH3 (homo-B) dimer remains uncomplexed and isdetected and quantified. In the embodiment in which both ACE assays arerun, both homodimers can be quantified. Here, the bispecific heterodimercan be quantified by substracting the quantity of each homodimerdetermined by the independent ACE assays from the total amount of dimer(CH3:CH3+CH3:CH3*+CH3*:CH3*) (homo-B+hetero-AB+homo-A) determined in aCZE assay without any ligand or using a standard curve that wasgenerated for spiked homo-A and/or homo-B samples.

The system and method in another embodiment uses a ligand plug insertednear the anode (loading) end of the capillary, between the loading portand the detector (PF-ACE). Here, the multimer mixture (comprising firsthomodimer, second homodimer, and heterodimer) is loaded onto thecapillary in front of the ligand plug. As the multimers migrate throughthe capillary, the constituent molecular entities encounter the ligandplug, at which point ligand-multimer complexes form, thereby reducingelectrophoretic mobility of all species except those homodimers that donot bind the ligand. When the ligand binds the first subunit, thehomodimer comprising two second subunits (and no first subunit) remainsunbound and has unaffected electrophoretic mobility.

According to some embodiments in which the heterodimer is a bispecificantibody, the first subunit is an immunoglobulin heavy chain capable ofbinding protein A (a.k.a. subunit-B), and the second subunit is animmunoglobulin heavy chain containing a H95R and Y96F substituted CH3domain (i.e., CH3*) (a.k.a. subunit-A), the ligand that binds to thefirst subunit is an antibody comprising heavy chain complementaritydetermining regions (HCDR) 1, 2 and 3, which comprise the amino acidsequences set forth in SEQ ID NO:1, SEQ ID NO:2, and SEQ ID NO:3,respectively, and comprising light chain complementarity determiningregions (LCDR) 1, 2 and 3, which comprise the amino acid sequences setforth in SEQ ID NO:4, SEQ ID NO:5, and SEQ ID NO:6, respectively. Here,the ligand that binds to the second subunit is an antibody comprisingheavy chain complementarity determining regions (HCDR) 1, 2 and 3, whichcomprise the amino acid sequences set forth in SEQ ID NO:7, SEQ ID NO:8,and SEQ ID NO:9, respectively, and comprising light chaincomplementarity determining regions (LCDR) 1, 2 and 3, which comprisethe amino acid sequences set forth in SEQ ID NO:10, SEQ ID NO:11, andSEQ ID NO:12, respectively.

EXAMPLES Example 1: Purity by Capillary Zone Electrophoresis (CZE)

To evaluate the purity of a bispecific antibody (“bsAb”), CE-SDS wasperformed under reduced conditions. CE-SDS results obtained for bsAb(heterodimer), homo-A (second homodimer) and homo-B (first homodimer)samples (FIG. 2, traces a-c) under reduced conditions revealed threepeaks corresponding to light chain (FIG. 2, peak-1), non-glycosylatedheavy chain (FIG. 2, peak-2) and heavy chain (FIG. 2, peak-3).Co-mixture sample of homo-A:bsAb1:homo-B (1:2:1 molar ratios) that wasprepared by spiking homo-A and homo-B to the purified bsAb1 alsoresulted in three peaks with similar migration times (FIG. 2, trace d).The electropherograms for bsAb, homodimers and their co-mixture were notdistinguishable, indicating a limitation of this size based separationmethod (FIG. 2). Similar results were observed for CE-SDS undernon-reducing conditions. These results are not surprising as theantibodies tested possess very similar molecular weights. Adequateseparation selectivity is critical to resolve these homodimericcomponents from bsAb.

CZE has been proven to be a powerful tool to resolve closely relatedmAbs (He, 2010). Purity of bsAb1 was assessed by CZE, a method thatseparates analytes based on their charge to size ratio. Analytes with agreater charge to size ratio migrate faster through the capillary.Relative to the pure bsAb-1 sample (FIG. 3, trace a), homo-A, with alarger charge to size ratio, migrates faster through the capillary (FIG.3, trace b). Homo-B, with a lower charge to size ratio, migrates slowerthrough the capillary (FIG. 3, trace c). As bsAb contains one arm of theheavy chain from homo-A (chain-A), and the other from homo-B (chain-B),and has a corresponding pI (8.01), the electrophoretic mobility of thebsAb lies between homo-A and homo-B (FIG. 3, trace a). The main peakgroup 2, 3 and 4 correspond to the homo-A, bsAb, and homo-Brespectively. The minor peaks observed in the electropherograms arisefrom either charge variants or size variants of antibodies. A mixture ofhomo-A, bsAb, and homo-B (1:2:1 ratio) was made by spiking homo-A andhomo-B to the purified bsAb. The mixture was then analyzed by CZE. TheCZE trace of the mixture contains four sets of peaks, representinghomo-A (peak group-2), bsAb (peak group-3), and homo-B (peak group-4)(FIG. 3, trace-d). The lower peak intensity observed for homo-B peakcould be attributed to a combination of slower electrophoretic mobilityand multiple charge variants of homo-B species that are distributedacross the electropherogram. The co-mixture of homo-A:bsAb1:homo-B, thathad no separation in CE-SDS (FIG. 2) showed promising results in CZE.The CZE profile for the bsAb1 (FIG. 3) is well resolved and thus theidentification and quantification of purity is promising. CE-SDSseparation was performed on an Agilent Bioanalyzer using Agilent Protein230 kit.

Example 2: Purity by Partial-Filled Affinity Capillary Electrophoresis

The CZE is limited to samples containing entities with diverse charge tosize ratios. Since this is not always the case, CZE cannot be applied tomany bsAb candidates. For instance, bsAb2 and related homodimers possesssimilar pIs and size, and hence share very similar CZE profiles (FIG. 4,traces a-c). Due to lack of separation of the various molecularentities, identification of individual component molecular species wasnot practical.

Another viable approach to quantify purity is affinity capillaryelectrophoresis (ACE). In ACE, a mixture of an antibody (Ab) and aligand (L), which forms an antibody-ligand complex (Ab·L), is prepared(see equation 1). The mixture is then injected into the capillary andelectrophoresed. ACE is based on the differences in electrophoreticmobility between Ab, L and Ab·L. When either antigen or a chain specificantibody is used as a ligand, the homodimer quantification becomesindependent of baseline resolution between various species. Theselective mobility shift of individual species can be used to estimatethe amount of any residual homodimers.

Ab+L

Ab·L  (1)

In ACE, an antigen can be used as a ligand for a cognate antibody.Alternatively, a chain specific antibody (anti-A or anti-B) can be usedas the ligand for the cognate antibody. Anti-A antibody (a.k.a., “secondligand”) binds specifically to an antibody that contains chain-A (homo-Aand bsAb). Similarly, anti-B antibody (a.k.a., “first ligand”) binds toan antibody containing chain-B (homo-B and bsAb).

In one embodiment, the anti-A antibody comprises heavy chain and lightchain CDRs having amino acid sequences of SEQ ID NOs:7-12. In oneembodiment, the anti-A antibody comprises a heavy chain variable regioncomprising the amino acid sequence of SEQ ID NO:13, and a light chainvariable region comprising the amino acid sequence of SEQ ID NO:14. Inone embodiment, the anti-A antibody comprises an immunoglobulin heavychain comprising the amino acid sequence of SEQ ID NO:15, and animmunoglobulin light chain comprising the amino acid sequence of SEQ IDNO:16.

In one embodiment, the anti-B antibody comprises heavy chain and lightchain CDRs having amino acid sequences of SEQ ID NOs:1-6. In oneembodiment, the anti-B antibody comprises a heavy chain variable regioncomprising the amino acid sequence of SEQ ID NO:17, and a light chainvariable region comprising the amino acid sequence of SEQ ID NO:18. Inone embodiment, the anti-A antibody comprises an immunoglobulin heavychain comprising the amino acid sequence of SEQ ID NO:19, and animmunoglobulin light chain comprising the amino acid sequence of SEQ IDNO:20.

In one embodiment, the theoretical isoelectric points (pIs) ofchain-A-specific and chain-B-specific antibodies are 6.55 and 6.64respectively. Peaks arising from analytes (bsAb or homodimers) thatpossess a similar pI and size could co-migrate with chain-specific mAbsand interfere with the identification and quantification. To avoid thispotential interference, the electrophoretic mobilities of chain specificantibodies were modified through biotinylation. The EZ-Link™Sulfo-NHS-Biotin kit and procedure (Thermo Scientific, Rockford, Ill.)were used to biotinylate anti-A and anti-B antibodies (Daniels andAmara, (1998) 296 Methods Enzymol. 307-18; Thermo Scientific,Instructions: EZ-Link™ Sulfo-NHS-biotin, Doc. No. 1850.3, available athttps://tools.lifetechnologies.com/content/sfs/manuals/MAN0011580_EZ_Sulfo_NHS_Biotin_UG.pdf,Apr. 29, 2015). Several different NHS esters of biotin with varyingproperties and spacer arm lengths are available. Briefly,N-Hydroxysuccinimide (NETS) esters of biotin (e.g., Sulfo-NHS-Biotin,which is water soluble) were reacted in pH 7-9 buffers with primaryamino groups (—NH2) of lysine and those available at the N-termini ofeach polypeptide.

Biotinylation via primary amine coupling and lysine side chainmodification altered the charge of the chain specific antibodies towardsthe acidic and therefore their electrophoretic velocities were reduced,resulting in loss of detectable signal within experimental run time. Theabsence of any detectable peaks from chain specific antibodies made theidentification and quantification of molecular species of intereststraightforward.

For ACE analysis, either anti-A or anti-B antibodies were used asligands. ACE was performed using a bsAb-ligand complex prepared bymixing bsAb3 and anti-A or anti-B antibodies at a molar ratio of 1:2.Upon complex formation, the electrophoretic mobility of bsAb3 wasexpected to be modified, and it was anticipated that no residual signalof free bsAb3 would remain. However, for bsAb3-anti-A and bsAb3-anti-Bcomplexes large amounts of residual peaks were detected at a similarmigration time to that of free bsAb3 (FIG. 5, traces b and c). ACE dataobtained for various ratios of bsAb and anti-B complexes (1:0.5, 1:1 and1:3) demonstrated that the residual peak was seen even in the presenceof excess anti-B ligand. To further investigate if residual unboundbsAb3 was present in the bsAb3-anti-B complex preparation, an SE-HPLCexperiment was performed where good resolution between bsAb3 (FIG. 6,trace a; peak 4) and anti-B (FIG. 6, trace b; peak 3) was noted. SE-HPLCresults indicate the presence of bsAb3-anti-B complex (FIG. 6, trace c;peaks 1 and 2) and excess anti-B (FIG. 6, trace c; peak 3). However,there is little to no evidence for the presence of any unbound bsAb3.These results suggest that the presence of residual peaks in high levelscould be attributed to the dissociation of analyte-ligand (e.g.,bsAb·L→bsAb+L) at high voltage applied during CZE experiments (FIG. 5).Dissociation of analyte-ligand complex has been previously reported inaffinity-based separation methods such as CE (S. Krylov, (2006) 11(2) JBiomol Screen 115-122). Previous attempts to separate an equilibriummixture containing ssDNA and ssDNA binding protein in a capillary wasfound to undergo continuous dissociation resulting in peaks andexponential “smears”. Both ligand and target were dissociated throughoutthe electrophoresis (Id). For some bsAbs, the presence of residual peaksand “smears” observed in ACE analysis interferes with purity analysis.

To circumvent the dissociation effects, Partial-Filled AffinityCapillary Electrophoresis (PF-ACE) was developed and utilized (Brown etal., 540 Analytica Chimica Acta 403-410(2005)). PF-ACE is performed bypartially filling the capillary with the ligand prior to sampleinjection. As the analytes migrate through the affinity ligand zone, aligand-analyte complex is formed and its mobility is shifted compared tofree analyte. The mobility of any residual analyte that does not bindthe affinity ligand remains unchanged. PF-ACE can therefore provide anaccurate estimate of the relative abundances of any residual analytepresent in a bsAb.

Experiments were run and data was collected for bsAb3-anti-B complexunder ACE and PF-ACE conditions. Residual bsAb3 peaks that were observedunder ACE conditions due to dissociation of analyte-ligand complex werenot detected in PF-ACE conditions (FIG. 7). Under ACE conditions, oncethe analyte dissociates from analyte-ligand complex it can no longerform the complex again. Under PF-ACE conditions, the migration ofanalyte through the ligand plug allows the analyte to re-formanalyte-ligand complex even if the analyte is dissociated earlier. Thehomo-B peaks that were observed in the absence of an affinity ligandzone, were shifted and shown as loss of signal when PF-ACE was performedwith anti-B mAb (FIG. 8, traces A and B). This effect is due tohomo-B-anti-B mAb complex formation. In contrast, the migration of thehomo-B mAb through a capillary partially filled with an anti-A mAbremains unchanged relative to the trace that contains no affinity ligandzone, as homo-B mAb does not bind anti-A mAb (FIG. 8, traces A, C).Similarly, mobility shifts were observed only for specific binding (i.e.homo-A+anti-A or homo-B+anti-B) and not by other ligands (FIG. 8, tracesD and F). These results indicate that the PF-ACE assay is highlyspecific to chain specific ligand based mobility shifts.

Example 3: Detection and Quantification of Homodimer mAb in BispecificSamples

To assess bsAb purity via PF-ACE assay, small amounts of (5%) of homo-Aand homo-B were spiked into a bsAb3 sample to serve as homodimer“impurities”. Resulting CZE and PF-ACE traces are shown in FIG. 9. Trace‘a’ shows the electropherogram of bsAb3. Trace ‘b’ shows theelectropherogram of bsAb3 spiked with 5% homo-A and homo-B impurities.Spiking of the homo-A and homo-B into bsAb3 resulted in an increase inthe intensities of two peaks (compare trace a and trace b, peaks 2 and4). Based on the electrophoretic mobilities of purified homodimers,these two peaks were tentatively identified, as homo-A and homo-Brespectively. These identities were confirmed upon PF-ACE experiments intraces c and d. Trace d shows the bsAb3-anti-B PF-ACE where residualpeaks would represent homo-A species. The residual peak observed in dhas a migration time similar to peak 2 in trace b, thus verifying theidentity of the peak in the spiked sample. Similar results were observedfor bsAb3-anti-A PF-ACE (FIG. 9, trace c, homo-B). A small amount ofresidual peak observed in FIG. 9, trace c was excluded from thequantification as it corresponds to a contaminant observed in bsAb3 andit is not coming from the spiked samples. Based on PF-ACE, the amount ofhomo-A and homo-B present in spiked samples were estimated to be 5.2%and 5.2% respectively. These values are in good agreement with thespiked amount of 5% and are within the experimental errors.

To assess limit of detection (LOD) and limit of quantification (LOQ),spike recovery was performed adding various amounts of homo-A and homo-Bto purified bsAb3. Nine bsAb3 samples containing wide range of homo-Aand homo-B mAbs (0.1%-5% by concentration) were prepared to study thelevel of homodimers present in these spiked samples. PF-ACE traces ofbsAb3 containing homo-A and homo-B in the absence of an affinity ligandresulted in an electropherogram comprising peaks corresponding to bsAb3,homo-A and homo-B. The electropherograms indicate the existence ofhomodimeric mAbs in each spiked bsAb3 samples. Excellent linear response(R²=0.999) was observed for homo-A (FIG. 10) and homo-B (FIG. 11) withincreasing concentrations in spiked bsAb3 samples. Overall, thehomodimer LOQ was experimentally determined to have a value of 0.1%.

Example 4: Protein Analysis Methodology

CZE experimentation was performed using a Beckman PA800 plus instrumentequipped with diode array detector. 32 Karat® software (Beckman Coulter,Inc., Brea, Calif.) was used for data analysis. Briefly, antibodysamples (1 mg/mL) were diluted with water to a concentration ofapproximately 1 mg/mL and injected at 0.5 psi for 45 seconds using aBeckman PA800 Plus with a bare fused silica capillary (total length of60.2 cm, effective length of 50 cm, i.d. of 40 μm). ACE was performedunder the same condition using a 1:2 molar ratio of bsAb to ligand. ForPF-ACE analysis, the ligand plug (2 mg/mL of modified ligand in 1×phosphate buffered saline) was injected for 90 seconds at 1 psi prior toanalyte or analyte-ligand complex injection. The separation wasperformed at 28 kV and the capillary temperature was maintained at 22°C. during separation. The samples were stored at 10° C. A buffercontaining 600 mM ε-aminocaproic acid-acetic acid, 0.1% HPMC, pH 5.7 wasused as a background electrolyte and 1 mM histidine was spiked as aninternal standard.

BsAb, homo-A and homo-B samples were analyzed by CE-SDS under reducingconditions. BsAb and homodimers were co-expressed and purified from asingle batch. Separation was performed on an Agilent Bioanalyzer andsample preparation generally followed the manufacturer's protocols forthe Protein 230 kit.

The antibody, ligand and antibody-ligand complex samples were alsoanalyzed based on size under native conditions by injection onto aWATERS ACQUITY UPLC system, equipped with ACQUITY UPLC BEH column(Waters Corporation, Milford, Mass.) that was equilibrated in SEC buffer(200 mM sodium phosphate, pH 7.1) at a flow rate of 0.3 mL/min.

1.-69. (canceled)
 70. A composition, comprising: a mixture of proteinsfor separating and detecting a first protein from one or more otherproteins in the mixture, wherein the composition includes: a firstprotein, one or more other proteins, and a modified ligand that does notbind to the first protein but is capable of binding to the one or moreother proteins to form a protein-ligand complex with a lower charge tomass ratio than the one or more other proteins without the modifiedligand; wherein the modified ligand has a lower isoelectric point thanan unmodified ligand.
 71. The composition of claim 70, wherein themodified ligand comprises an acidic moiety.
 72. The composition of claim70, wherein the first protein is a multi subunit protein, wherein theone or more other proteins is a multi subunit protein, and wherein thefirst protein and the one or more other proteins have similar charge tomass ratios.
 73. The composition of claim 70, wherein the first proteincomprises two identical first subunits, wherein the one or more otherproteins comprises two identical second subunits or a combination of thefirst subunit and the second subunit, wherein the modified ligand iscapable of binding to the second subunit.
 74. The composition of claim70, wherein the modified ligand comprises a covalent linkage with alysine residue on the modified ligand.
 75. The composition of claim 70,wherein the modified ligand comprises one or more amino acid sequencesselected from the group consisting of SEQ ID NO:1, SEQ ID NO:2, SEQ IDNO:3, SEQ ID NO:7, SEQ ID NO:8 and SEQ ID NO:9.
 76. The composition ofclaim 70, wherein the first protein is a first bivalent monospecificantibody and the mixture of proteins comprises a bispecific antibody anda second bivalent monospecific antibody.
 77. A system comprising: acapillary for housing a composition; a detector coupled to thecapillary; an anode at or near one end of the capillary; a cathode at ornear the other end of the capillary; and a power supply coupled to thecapillary; wherein the composition is a mixture of proteins including afirst protein, one or more other proteins, and a modified ligand thatdoes not bind to the first protein but is capable of binding to the oneor more other proteins to form one or more protein-ligand complexes witha lower charge to mass ratio than the one or more other proteins withoutthe modified ligand; and wherein the modified ligand has a lowerisoelectric point than an unmodified ligand.
 78. The system of claim 77,wherein the modified ligand comprises an acidic moiety.
 79. The systemof claim 77, wherein the first protein is a multi subunit protein,wherein the one or more other proteins is a multi subunit protein, andwherein the first protein and the one or more other proteins havesimilar charge to mass ratios.
 80. The system of claim 77, wherein themodified ligand comprises a covalent linkage with a lysine residue onthe modified ligand.
 81. The system of claim 77, wherein the modifiedligand comprises one or more amino acid sequences selected from thegroup consisting of SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:7,SEQ ID NO:8 and SEQ ID NO:9.
 82. The system of claim 77, wherein thedetector is positioned near the cathode end of the capillary and theprotein mixture is positioned in the capillary at the anode end of thecapillary.
 83. The system of claim 77, wherein the detector detects 200nm to 280 nm light absorbance or laser induced fluorescence.
 84. Thesystem of claim 77, wherein the capillary comprises a ligand plugpositioned between the anode and the detector, and the ligand plugcomprises the modified ligand.
 85. The system of claim 77, wherein thefirst protein is a first bivalent monospecific antibody and the mixtureof proteins comprises a bispecific antibody and a second bivalentmonospecific antibody.